The Long Island Rail Road’s former police chief — who left under a cloud a year ago for personal use of agency property — has resurfaced as Amtrak’s top New York cop.

John O’Connor is now Amtrak’s police inspector overseeing 100 cops in New York and New Jersey from Penn Station.

Amtrak hired O’Connor despite an investigation by the MTA inspector general that found he had given his daughter one of the LIRR’s IBM laptop computers for her personal use while at Harvard, and permitted his other daughter and wife to use another laptop at home.

The report also rapped O’Connor for lying on LIRR travel reports to conceal using his assigned agency car to take his daughter to and from college in Massachusetts, and filling the tank for these trips with an agency credit card.

The actions violated LIRR policies, the New York state ethics law and “may have” broken the state penal law, MTA Inspector General Roland Malan said in the Dec. 22, 1997, report.

The report indicates that the LIRR “asked” for O’Connor’s resignation, but transit sources said he was kept around long enough to qualify for a hefty pension after 25 years of service. The LIRR and Metro-North police were merged into the Metropolitan Transportation Authority police department in 1998.

Shortly thereafter, Amtrak — which along with the LIRR operates out of Penn Station — hired O’Connor as a consultant to oversee security issues for new Acela high-speed train programs.

In a statement, Amtrak said it recently promoted O’Connor to head the New York-New Jersey division “based on performance.”

“Inspector O’Connor enjoys the respect and confidence of management and his employees,” Amtrak said.

Union officials representing LIRR cops were livid.

“O’Connor was a real disciplinarian. He held everyone to a high standard — except himself,” said Ray Gimmler, president of the MTA Patrolmen’s Benevolent Association.

He complained that rank-and-file cops caught taking railroad property would have been “taken away in handcuffs.”

Officials with the Metropolitan Transportation Authority and the LIRR had no immediate comment, and neither did O’Connor.